The term “reproducibility” conjures a mental image of dedicated systems
conducting automated and repeatable computations. However, you can
embrace reproducibility as a principle to apply to your day-to-day
research activities. Neuroimaging is a heavily data and software driven
field of science. As a result, by learning more tricks and techniques
of the tools that you already use daily, you will discover ways to
not only improve efficiency but also increase the reproducibility of
your research.

This module guides through three somewhat independent topics, which
are in the heart of establishing and efficiently using common generic
resources: command line shell, version control systems (for code and
data), and distribution package managers. It is very unlikely that you have
managed to avoid those tools completely in your prior research activities, but it
is possible that you have under-utilized the power they are providing.
Gaining additional skills in any of those topics could help you to not
only become more efficient in your day-to-day research activities, but
also would lay foundation in establishing habits to make your work
actually more reproducible. Moreover these topics will be in the
foundation of future modules in the ReproNim curriculum.

To some degree, reproducibility requires knowledge of what,
when, and how any particular analysis was carried out.
Therefore materials in this module will focus on helping to
answer those questions. Before addressing these specific questions,
referenced external materials (tutorials, lessons, etc) will provide a
more generic and more thorough presentation of the topics.

Prerequisites

Depending on your level of competence in any particular topic, you
might like to go through additional materials which will be
referenced in each particular lesson. Even if you feel that you are
very proficient in all of those topics, we hope you would still
learn some new “tricks” or would recommend or contribute some new
materials to the lessons.